Hi freesurfer team,
I think this is a very basic error with the mri_convert command but I can't
seem to make it work, I'm getting this:
mri_convert $PWD 001.nii
mri_convert
/Applications/freesurfer/subjects/DEM009/dicom/20140731/1835 001.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:1
hi guys i'm getting a 'Couldn't create output file .xdebug_tkmedit' before
loading volumes, any suggestions on what I can do would be most welcome.
Also got:
ERROR: A segfault has occurred. This is not your fault,
: but is most likely an unrecoverable error and has
: made the program unstable.
Hi freesurfer crew,
I found some details through this website
http://www.stat.uchicago.edu/faculty/InMemoriam/worsley/research/surfstat/index.htm
about
cortical thickness maps with freesurfer. I have done some reading but can't
really make much sense of how I might do this for a single subject thr
Hi guys, just wondering what you'd say is the best measure for whole brain
volume? Cortex volume.. Cortical white matter volume.. Total gray volume..
Intracranial volume.. etc.
Cheers!
Hugh
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Hi,
So when using command tkmedit *subjID* brainmask.mgz -aux -wm.mgz -surfs I
receive the message:
"Error: Parsing -aux option
Expected an argument
This option needs an argument: the image type, directory, or file name of
the data to load as the aux volume."
My apologies if there is an obvious
Hi,
I have resolved the issue below, apologies, was a stupid question!
Thanks,
Hugh
On 1 August 2012 15:59, Hugh Pemberton wrote:
> Hi,
>
> So when using command tkmedit *subjID* brainmask.mgz -aux -wm.mgz -surfs I
> receive the message:
>
> "Error: Parsing -aux option
Hi,
How can I get sulcal depth measurements from Freesurfer?
Cheers,
Hugh
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The information in this e-mail is intended only for the p
> step before the segmentation. "Normalization" is also refers to
> intersubject registration. Probably you mean the latter.
> doug
>
>
>
> On 08/13/2012 09:56 PM, Hugh Pemberton wrote:
>
>> Hi Doug,
>>
>> Thanks so much for getting back to my or
achine?
>
>
>
> On Aug 28, 2012, at 10:17 PM, Hugh Pemberton wrote:
>
>> Hi Freesurfers,
>>
>> Have had this error come up after recon-all for a number of subjects and was
>> wondering if you know what the issue is..? I have attached the recon-all.log
>>
Dear freesurfer crew,
I'm having a few issues with segmentation around the hippocampus, I have
included a few screenshots of main and aux vol where the hippocampus has
been excluded even with the addition of control points. Have you got any
tips for rectifying this? It's happened a fair few times
Hi,
I have just received this error after a recon-all subjid- ___ all :
ERROR: _FindFacePath: could not find path!
/home/hughp/freesurfer/subjects/B__/scripts
mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
intersection removal took 0.00 hours
removing intersecting faces
w
Hi Hugh
> This is fixed in the newest version. What version are you running?
> Bruce
>
>
>
> On Nov 15, 2012, at 6:48 PM, Hugh Pemberton
> wrote:
>
> Hi,
>
> I have just received this error after a recon-all subjid- ___ all :
>
> ERROR: _FindFacePath: could no
uce Fischl wrote:
> this is a bug in the topology fixer. Maybe Zeke or Nick can post a new
> version of it? Was it mris_topo_fixer that was runing or mris_fix_topology?
>
> On Fri, 16 Nov 2012, Hugh Pemberton wrote:
>
> Hi Bruce,
>> Thanks for getting back to me.
5.1.0
On 28 November 2012 13:59, Bruce Fischl wrote:
> What version are you running?
>
>
>
> On Nov 27, 2012, at 8:51 PM, Hugh Pemberton
> wrote:
>
> Generally about 4 or 5 slices away, no other images unfortunately! Any
> ideas or is the atrophy just too great?
etter
> >
> >
> >
> >
> > On Nov 27, 2012, at 10:44 PM, Hugh Pemberton
> > wrote:
> >
> >
> >
> > > 5.1.0
> > >
> > >
> > >
> > >
> > > On 28 November 2012 13:59, Bruce Fisch
Hi, did anyone have a chance to see my last e mail? See below, cheers!
Hugh
On 16 November 2012 10:48, Hugh Pemberton wrote:
> Hi,
>
> I have just received this error after a recon-all subjid- ___ all :
>
> ERROR: _FindFacePath: could not find path!
> /home/hughp/f
that'd great, cheers!
Hugh
On 5 December 2012 10:29, Bruce Fischl wrote:
> Hi Hugh
>
> this is fixed in 5.2. If you need a fix right away Nick or Zeke can get
> you an updated mris_topo_fixer binary
>
> cheers
> Bruce
>
>
> On Wed, 5 Dec 2012, Hugh Pemberto
Hi, I'm getting the following error when trying to use the asegstats2table
command, I can't see anything similar from previous emails, any ideas what
the issue is? Thanks v much in advance.
asegstats2table --subjects baseline 12m 24m 36m --meas volume --tablefile
aseg_stats.txt
File "/Applicati
Hi everyone,
I was wondering if someone could comment on which portion of the precentral
gyrus is used to produce subcortical volume stats? Is it just medial or
lateral the whole gyrus?
Many thanks and all the best,
Hugh
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Hi everyone,
I was wondering if someone could comment on which portion of the precentral
gyrus is used to produce subcortical volume stats? Is it just medial or
lateral the whole gyrus?
Many thanks and all the best,
Hugh
On 5 June 2014 12:25, Hugh Pemberton wrote:
> Hi everyone,
>
&
On 6 June 2014 12:00, Hugh Pemberton wrote:
> Hi everyone,
>
> I was wondering if someone could comment on which portion of the
> precentral gyrus is used to produce subcortical volume stats? Is it just
> medial or lateral the whole gyrus?
>
> Many thanks and all the best,
&
Hi everyone, I'm getting the follow error and it's jus started happening
after updating Xquartz.. any ideas what I can do? Also, i dont have a
.debug_tkmedit file, when tkmedit was running normally the first line would
say could not create debug file.
Many thanks,
Hugh
ERROR: A segfault has occur
p/launch-ivIjwf/org.macosforge.xquartz:0
On 14 July 2014 09:41, Hugh Pemberton wrote:
> Hi everyone, I'm getting the follow error and it's jus started happening
> after updating Xquartz.. any ideas what I can do? Also, i dont have a
> .debug_tkmedit file, when tkmedit was run
ld be much
appreciated.
Many thanks,
Hugh
On 14 July 2014 15:25, Hugh Pemberton wrote:
> i've tried reinstalling xquartz (this is on a mac by the way) and now I'm
> getting this error when trying to run tkmedit, any ideas would be hugely
> appreciated!
>
> Thanks,
>
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